Set non-detects and unquantified values in residue series without replicates

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This function automates replacing unquantified values in residue time and -depth series. For time series, the function performs part of the residue -processing proposed in the FOCUS kinetics guidance for parent compounds -and metabolites. For two-dimensional residue series over time and depth, -it automates the proposal of Boesten et al (2015).

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set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
-
-set_nd_nq_focus(
-  res_raw,
-  lod,
-  loq = NA,
-  set_first_sample_nd = TRUE,
-  first_sample_nd_value = 0,
-  ignore_below_loq_after_first_nd = TRUE
-)

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Arguments

res_raw: Character vector of a residue time series, or matrix of -residue values with rows representing depth profiles for a specific sampling -time, and columns representing time series of residues at the same depth. -Values below the limit of detection (lod) have to be coded as "nd", values -between the limit of detection and the limit of quantification, if any, have -to be coded as "nq". Samples not analysed have to be coded as "na". All -values that are not "na", "nd" or "nq" have to be coercible to numeric
lod: Limit of detection (numeric)
loq: Limit of quantification(numeric). Must be specified if the FOCUS rule to -stop after the first non-detection is to be applied
time_zero_presence: Do we assume that residues occur at time zero? -This only affects samples from the first sampling time that have been -reported as "nd" (not detected).
set_first_sample_nd: Should the first sample be set to "first_sample_nd_value" -in case it is a non-detection?
first_sample_nd_value: Value to be used for the first sample if it is a non-detection
ignore_below_loq_after_first_nd: Should we ignore values below the LOQ after the first -non-detection that occurs after the quantified values?

Value

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A numeric vector, if a vector was supplied, or a numeric matrix otherwise

Functions

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set_nd_nq_focus(): Set non-detects in residue time series according to FOCUS rules

References

Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. -J. and Pol, J. W. (2015). Leaching of plant protection products and their -transformation products; Proposals for improving the assessment of leaching -to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra -Wageningen UR (University & Research centre)

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation -Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, -18 December 2014, p. 251

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Examples

# FOCUS (2014) p. 75/76 and 131/132
-parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-set_nd_nq(parent_1, 0.02)
-#>  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA
-parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-set_nd_nq(parent_2, 0.02)
-#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01   NA   NA
-set_nd_nq_focus(parent_2, 0.02, loq = 0.05)
-#>  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA
-parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-set_nd_nq(parent_3, 0.02)
-#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA
-set_nd_nq_focus(parent_3, 0.02, loq = 0.05)
-#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA
-metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-set_nd_nq(metabolite, 0.02)
-#>  [1]   NA   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA
-set_nd_nq_focus(metabolite, 0.02, 0.05)
-#>  [1] 0.00   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA
-#
-# Boesten et al. (2015), p. 57/58
-table_8 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nq", 2), rep("nd", 2),
-    10, 10, 10, "nq", "nd", "nd",
-    "nq", 10, "nq", rep("nd", 3),
-    "nd", "nq", "nq", rep("nd", 3),
-    rep("nd", 6), rep("nd", 6)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
-#>       [,1]  [,2]  [,3] [,4] [,5] [,6]
-#> [1,] 10.00 10.00  0.25 0.25   NA   NA
-#> [2,] 10.00 10.00  1.00 1.00 0.25   NA
-#> [3,] 10.00 10.00 10.00 1.00 0.25   NA
-#> [4,]  1.00 10.00  1.00 0.25   NA   NA
-#> [5,]  0.25  1.00  1.00 0.25   NA   NA
-#> [6,]    NA  0.25  0.25   NA   NA   NA
-#> [7,]    NA    NA    NA   NA   NA   NA
-table_10 <- matrix(
-  c(10, 10, rep("nd", 4),
-    10, 10, rep("nd", 4),
-    10, 10, 10, rep("nd", 3),
-    "nd", 10, rep("nd", 4),
-    rep("nd", 18)),
-  ncol = 6, byrow = TRUE)
-set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
-#>       [,1]  [,2]  [,3] [,4] [,5] [,6]
-#> [1,] 10.00 10.00  0.25   NA   NA   NA
-#> [2,] 10.00 10.00  0.25   NA   NA   NA
-#> [3,] 10.00 10.00 10.00 0.25   NA   NA
-#> [4,]  0.25 10.00  0.25   NA   NA   NA
-#> [5,]    NA  0.25    NA   NA   NA   NA
-#> [6,]    NA    NA    NA   NA   NA   NA
-#> [7,]    NA    NA    NA   NA   NA   NA
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